Multi-Omics Reveal Immune Microenvironment Alterations in Multiple Myeloma and Its Precursor Stages

Introduction: Tumor immune microenvironmental alterations occur early in multiple myeloma (MM) development. Deep molecular characterization of the immune profiles and their crosstalk with tumor cells in MM and its precursor conditions is needed to advance treatment development and discover safe and efficient strategies to prevent disease progression. In this study, we aim to systematically characterize the tumor immune microenvironment (TME) and the tumor-immune interactions from precursor stages, i.e., monoclonal gammopathy of undetermined significance (MGUS) and smoldering MM (SMM), to newly diagnosed MM, comparing these to healthy donors. Methods: Most current studies rely on BM aspirates, which often get contaminated by peripheral blood and lose mature granulocytes during processing. To address this limitation, we evaluated the BM cell content using a whole BM gene expression-based computational technique, CIBERSORT, and investigated the correlation of immune cell proportions with patient outcome after 5-20 years of follow-up. We also analyzed BM immune cell functional marker expression using mass cytometry in a large cohort of patients and examined BM immune cell gene expression in paired stable or progressive MM precursor conditions and MM samples using single-cell RNA sequencing (sc-RNA seq). Results: By integrating results from CIBERSORT, mass cytometry, and sc-RNA seq, we demonstrate an altered balance of innate and adaptive immunity persisting from MGUS to MM. Specifically, the proportion of neutrophils decreasing in the tumor microenvironment (TME), predicts SMM progression and MM outcomes. HLA-DR is reduced in CD16+ monocytes and plasmacytoid dendritic cells. Myeloid dendritic cells are also decreased, and their expression of stress and immune-response genes is inhibited in MM and its precursor stages. We find that NK cells and CD8 T cells show common features with a shift from GZMK+ to GZMB+ cytotoxic phenotype in the TME compared to normal BM and this is accompanied by increased expressions of inhibitory markers TIM3 and TIGIT. Finally, we show that patient-specific GZMB+ CD8 T cell subtypes demonstrate limited changes in paired precursor and MM samples despite the increased numbers and heterogeneity of MM subclones in overt MM. Conclusion: Overall, these results provide a comprehensive immune landscape of MM and its precursor stages. Enhancing neutrophil and NK cell cytotoxicity, tumor antigen presentation, and CD8 T cell versatility in precursor stages may prevent MM progression.